build problem with netcdf with ifort using mpi

[Ed Hartnett]

Howdy all!

I am a programmer for the netCDF package, an open source scientific data
package widely used in weather and climate research.

The latest version of netCDF is having a problem with intel compilers,
when using the MPI library (which, annoyingly, has a wrapper script
around the compiler.)

The daily snapshot of the netCDF library is here:
ftp://ftp.unidata.ucar.edu/pub/netcdf/snapshot/netcdf-4-daily.tar.gz

There are two failure modes. One happens on make install (after make
check completes successfully), and the other happens in make check.

Libtool then seems to issue a command to ifort that makes no sense. 

The output for the make check case looks like this:
make[2]: Entering directory
`/data/kb/compile/netcdf-4.1.3-rc1-snapshot2011052320/fortran'
/bin/bash ../libtool --tag=FC   --mode=link mpif90  -g  -version-number
5:1:0  -L/opt/hdf5-par/lib -o libnetcdff.la -rpath
/opt/netcdf-4.1.3-rc1-snapshot2011052320_IFORT-par/lib fort-attio.lo
fort-control.lo fort-dim.lo fort-genatt.lo fort-geninq.lo fort-genvar.lo
fort-lib.lo fort-misc.lo fort-v2compat.lo fort-vario.lo fort-var1io.lo
fort-varaio.lo fort-varmio.lo fort-varsio.lo fort-nc4.lo
../liblib/libnetcdf.la ../f90/libnetcdff90.la -lm -lhdf5_hl -lhdf5 -lz
-lm
libtool: link: mpif90 -shared   .libs/fort-attio.o .libs/fort-control.o
.libs/fort-dim.o .libs/fort-genatt.o .libs/fort-geninq.o
.libs/fort-genvar.o .libs/fort-lib.o .libs/fort-misc.o
.libs/fort-v2compat.o .libs/fort-vario.o .libs/fort-var1io.o
.libs/fort-varaio.o .libs/fort-varmio.o .libs/fort-varsio.o
.libs/fort-nc4.o   --whole-archive ../f90/.libs/libnetcdff90.a
--no-whole-archive  -rpath
/data/kb/compile/netcdf-4.1.3-rc1-snapshot2011052320/liblib/.libs -rpath
/opt/netcdf-4.1.3-rc1-snapshot2011052320_IFORT-par/lib
-L/opt/hdf5-par/lib ../liblib/.libs/libnetcdf.so -L/usr/lib
/usr/lib/libcurl-gnutls.so /opt/hdf5-1.8.6-par/lib/libhdf5_hl.a
/opt/hdf5-1.8.6-par/lib/libhdf5.a -lz -L/opt/mpich2-1.3.2p1-romio/lib
-L/data/opt/intel/composerxe-2011.2.137/compiler/lib/ia32
-L/data/opt/intel/composerxe-2011.2.137/mkl/lib/ia32
-L/usr/lib/gcc/i686-linux-gnu/4.4.5/
-L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../../../lib/ -L/lib/../lib/
-L/usr/lib/../lib/
-L/data/opt/intel/composerxe-2011.2.137/compiler/lib/ia32/
-L/data/opt/intel/composerxe-2011.2.137/mkl/lib/ia32/
-L/usr/lib/gcc/i686-linux-gnu/4.4.5/../../../ -L/lib/ -L/usr/lib/
-L/usr/lib/i686-linux-gnu -lmpichf90 -lmpich
/opt/mpich2-1.3.2p1-romio/lib/libopa.a
/opt/mpich2-1.3.2p1-romio/lib/libmpl.a -lrt -lpthread -lifport -lifcore
-limf -lsvml -lm -lipgo_pic -lintlc -lgcc_s -lirc_s -ldl -lc    -soname
libnetcdff.so.5 -o .libs/libnetcdff.so.5.1.0
ifort: command line warning #10006: ignoring unknown option
'-fwhole-archive'
ifort: command line warning #10006: ignoring unknown option
'-fno-whole-archive'
ifort: command line warning #10156: ignoring option '-r'; no argument
required
ifort: command line warning #10156: ignoring option '-r'; no argument
required
ifort: error #10236: File not found:
'/opt/netcdf-4.1.3-rc1-snapshot2011052320_IFORT-par/lib'


The output for the make install case looks like this:

> libtool: relink: ifort -shared -nofor_main  .libs/fort-attio.o
> .libs/fort-control.o .libs/fort-dim.o .libs/fort-genatt.o
> .libs/fort-geninq.o .libs/fort-genvar.o .libs/fort-lib.o
> .libs/fort-misc.o .libs/fort-v2compat.o .libs/fort-vario.o
> .libs/fort-var1io.o .libs/fort-varaio.o .libs/fort-varmio.o
> .libs/fort-varsio.o  -Wl,--whole-archive ../f90/.libs/libnetcdff90.a
> -Wl,--no-whole-archive  -Wl,-rpath
> -Wl,/apps/netcdf/4.1.3-rc1/intel/lib
> -L/apps/netcdf/4.1.3-rc1/intel/lib -lnetcdf -L/usr/kerberos/lib64
> -lcurl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto
> -lz -L/apps/intel/composerxe-2011.1.107/compiler/lib/intel64
> -L/apps/intel/composerxe-2011.1.107/ipp/../compiler/lib/intel64
> -L/apps/intel/composerxe-2011.1.107/ipp/lib/intel64
> -L/apps/intel/composerxe-2011.1.107/mkl/lib/intel64
> -L/apps/intel/composerxe-2011.1.107/tbb/lib/intel64//cc4.1.0_libc2.4_kernel2.6.16.21
> -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2
> -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64
> -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../.. -L/lib64 -L/lib
> -L/usr/lib64 -L/usr/lib -lifport -lifcore -limf -lsvml -lm -lipgo
> -lintlc -lpthread -lgcc_s -lirc_s -ldl -lc    -Wl,-soname
> -Wl,libnetcdff.so.5 -o .libs/libnetcdff.so.5.1.0
> /data/gerry/apps/netcdf-4.1.3-rc1-snapshot2011051306/libtool: line
> 8964: ifort: command not found
> libtool: install: error: relink `libnetcdff.la' with the above command
> before installing it
> make[3]: *** [install-libLTLIBRARIES] Error 1
> make[3]: Leaving directory
> /data/gerry/apps/netcdf-4.1.3-rc1-snapshot2011051306/fortran'
> make[2]: *** [install-am] Error 2
> make[2]: Leaving directory
> /data/gerry/apps/netcdf-4.1.3-rc1-snapshot2011051306/fortran'
> make[1]: *** [install] Error 2
> make[1]: Leaving directory
> /data/gerry/apps/netcdf-4.1.3-rc1-snapshot2011051306/fortran'
> make: *** [install-recursive] Error 1


-- 
Ed Hartnett  -- address@hidden